M. musculus 3 cell types, 1 timepoint, 3 genotypes, and 1 replicate.

1 M. musculus

This will be a very minimal analysis until we get some replicates.

1.1 Annotations

I am using mm38_95.

## My load_biomart_annotations() function defaults to human, so that will be quick.
mm_annot <- load_biomart_annotations(species="mmusculus")

## The biomart annotations file already exists, loading from it.

mm_annot <- mm_annot[["annotation"]]
mm_annot[["txid"]] <- paste0(mm_annot[["ensembl_transcript_id"]], ".", mm_annot[["version"]])
rownames(mm_annot) <- make.names(mm_annot[["ensembl_gene_id"]], unique=TRUE)

tx_gene_map <- mm_annot[, c("txid", "ensembl_gene_id")]

So, I now have 2 data frames of parasite annotations and 1 human.

1.2 Metadata

I am going to write a quick sample sheet in the current working directory called ‘all_samples.xlsx’ and put the names of the count tables in it.

1.3 Create expressionsets

Here I combine the metadata, count data, and annotations.

It is worth noting that the gene IDs from htseq-count probably do not match the annotations retrieved because they are likely exon-based rather than gene based. This is not really a problem, but don’t forget it!

mm38_expt <- create_expt("sample_sheets/all_samples.xlsx", tx_gene_map=tx_gene_map,
                         gene_info=mm_annot, file_column="salmonfile")

## Reading the sample metadata.

## The sample definitions comprises: 8 rows(samples) and 8 columns(metadata fields).

## Reading count tables.

## Using the transcript to gene mapping.

## Reading salmon data with tximport.

## Finished reading count tables.

## Matched 6764 annotations and counts.

## Bringing together the count matrix and gene information.

## The mapped IDs are not the rownames of your gene information, changing them now.

## Some annotations were lost in merging, setting them to 'undefined'.

## The final expressionset has 6764 rows and 8 columns.

mmtx_annot <- mm_annot
rownames(mmtx_annot) <- mm_annot[["txid"]]
mm38_tx <- create_expt("sample_sheets/all_samples.xlsx",
                         gene_info=mmtx_annot, file_column="salmonfile")

## Reading the sample metadata.

## The sample definitions comprises: 8 rows(samples) and 8 columns(metadata fields).

## Reading count tables.

## Reading salmon data with tximport.

## Finished reading count tables.

## Matched 6897 annotations and counts.

## Bringing together the count matrix and gene information.

## Some annotations were lost in merging, setting them to 'undefined'.

## The final expressionset has 56886 rows and 8 columns.

1.4 Query expressionsets

In this block I will calculate all the diagnostic plots, but not show them. I will show them next with a little annotation.

I will leave the output for the first of each invocation and silence it for the second.

mm38_plots <- graph_metrics(mm38_expt)

## Graphing number of non-zero genes with respect to CPM by library.

## Graphing library sizes.

## Graphing a boxplot.

## This data will benefit from being displayed on the log scale.

## If this is not desired, set scale='raw'

## Some entries are 0.  We are on log scale, adding 1 to the data.

## Changed 21398 zero count features.

## Graphing a correlation heatmap.

## Graphing a standard median correlation.

## Performing correlation.

## Graphing a distance heatmap.

## Graphing a standard median distance.

## Performing distance.

## Graphing a PCA plot.

## Graphing a T-SNE plot.

## Plotting a density plot.

## This data will benefit from being displayed on the log scale.

## If this is not desired, set scale='raw'

## Some entries are 0.  We are on log scale, setting them to 0.5.

## Changed 21398 zero count features.

## Plotting a CV plot.

## Naively calculating coefficient of variation/dispersion with respect to condition.

## Finished calculating dispersion estimates.

## Plotting the representation of the top-n genes.

## Plotting the expression of the top-n PC loaded genes.

## Printing a color to condition legend.

mm38_norm <- normalize_expt(mm38_expt, norm="quant", convert="cpm", transform="log2", filter=TRUE)

## This function will replace the expt$expressionset slot with:

## log2(cpm(quant(cbcb(data))))

## It will save copies of each step along the way
##  in expt$normalized with the corresponding libsizes. Keep libsizes in mind
##  when invoking limma.  The appropriate libsize is non-log(cpm(normalized)).
##  This is most likely kept at:
##  'new_expt$normalized$intermediate_counts$normalization$libsizes'
##  A copy of this may also be found at:
##  new_expt$best_libsize

## Not correcting the count-data for batch effects.  If batch is
##  included in EdgerR/limma's model, then this is probably wise; but in extreme
##  batch effects this is a good parameter to play with.

## Step 1: performing count filter with option: cbcb

## Removing 2794 low-count genes (3970 remaining).

## Step 2: normalizing the data with quant.

## Step 3: converting the data with cpm.

## Step 4: transforming the data with log2.

## transform_counts: Found 1105 values equal to 0, adding 1 to the matrix.

## Step 5: not doing batch correction.

mm38n_plots <- sm(graph_metrics(mm38_norm))

1.5 Show some plots

mm38_plots$legend

mm38_plots$libsize

mm38_plots$nonzero

mm38n_plots$density

mm38n_plots$pc_plot

1.6 Do a simple DE

The only interesting DE I see in this is to compare the retinas to the dlgns. I can treat them as replicates and compare.

mm <- set_expt_conditions(mm38_expt, fact="celltype")
mm_norm <- normalize_expt(mm, norm="quant",
                          convert="cpm", transform="log2", filter=TRUE)

## This function will replace the expt$expressionset slot with:

## log2(cpm(quant(cbcb(data))))

## It will save copies of each step along the way
##  in expt$normalized with the corresponding libsizes. Keep libsizes in mind
##  when invoking limma.  The appropriate libsize is non-log(cpm(normalized)).
##  This is most likely kept at:
##  'new_expt$normalized$intermediate_counts$normalization$libsizes'
##  A copy of this may also be found at:
##  new_expt$best_libsize

## Not correcting the count-data for batch effects.  If batch is
##  included in EdgerR/limma's model, then this is probably wise; but in extreme
##  batch effects this is a good parameter to play with.

## Step 1: performing count filter with option: cbcb

## Removing 2794 low-count genes (3970 remaining).

## Step 2: normalizing the data with quant.

## Step 3: converting the data with cpm.

## Step 4: transforming the data with log2.

## transform_counts: Found 1105 values equal to 0, adding 1 to the matrix.

## Step 5: not doing batch correction.

plot_pca(mm_norm)$plot

mm_de <- all_pairwise(mm, model_batch=FALSE)

## This function will replace the expt$expressionset slot with:

## log2(cpm(quant(cbcb(data))))

## It will save copies of each step along the way
##  in expt$normalized with the corresponding libsizes. Keep libsizes in mind
##  when invoking limma.  The appropriate libsize is non-log(cpm(normalized)).
##  This is most likely kept at:
##  'new_expt$normalized$intermediate_counts$normalization$libsizes'
##  A copy of this may also be found at:
##  new_expt$best_libsize

## Not correcting the count-data for batch effects.  If batch is
##  included in EdgerR/limma's model, then this is probably wise; but in extreme
##  batch effects this is a good parameter to play with.

## Step 1: performing count filter with option: cbcb

## Removing 2794 low-count genes (3970 remaining).

## Step 2: normalizing the data with quant.

## Step 3: converting the data with cpm.

## Step 4: transforming the data with log2.

## transform_counts: Found 1105 values equal to 0, adding 1 to the matrix.

## Step 5: not doing batch correction.

## Plotting a PCA before surrogates/batch inclusion.

## Not putting labels on the plot.

## Assuming no batch in model for testing pca.

## Not putting labels on the plot.

## Finished running DE analyses, collecting outputs.

## Comparing analyses.

dlgn_ko <- "iprgc_06"
dlgn_wt <- "iprgc_01"
dlgn_ht <- "iprgc_04"
scn_ko <- "iprgc_08"
scn_wt <- "iprgc_03"
retina_ko <- "iprgc_07"
retina_wt <- "iprgc_02"
retina_ht <- "iprgc_05"

het_retina_vs_het_dlgn <- exprs(mm38_norm)[, retina_ht] - exprs(mm38_norm)[, dlgn_ht]
ko_retina_vs_ko_dlgn <- exprs(mm38_norm)[, retina_ko] - exprs(mm38_norm)[, dlgn_ko]
ko_retina_vs_ko_scn <- exprs(mm38_norm)[, retina_ko] - exprs(mm38_norm)[, scn_ko]
het_retina_vs_ko_retina <- exprs(mm38_norm)[, retina_ht] - exprs(mm38_norm)[, retina_ko]
het_dlgn_vs_ko_scn <- exprs(mm38_norm)[, dlgn_ht] - exprs(mm38_norm)[, scn_ko]
ko_dlgn_vs_ko_scn <- exprs(mm38_norm)[, dlgn_ko] - exprs(mm38_norm)[, scn_ko]

dlgn_kowt <- exprs(mm38_norm)[, dlgn_ko] - exprs(mm38_norm)[, dlgn_wt]
dlgn_htwt <- exprs(mm38_norm)[, dlgn_ht] - exprs(mm38_norm)[, dlgn_wt]
dlgn_koht <- exprs(mm38_norm)[, dlgn_ko] - exprs(mm38_norm)[, dlgn_ht]
scn_kowt <- exprs(mm38_norm)[, scn_ko] - exprs(mm38_norm)[, scn_wt]
retina_kowt <- exprs(mm38_norm)[, retina_ko] - exprs(mm38_norm)[, retina_wt]
retina_htwt <- exprs(mm38_norm)[, retina_ht] - exprs(mm38_norm)[, retina_wt]
retina_koht <- exprs(mm38_norm)[, retina_ko] - exprs(mm38_norm)[, retina_ht]

pair_mtrx <- cbind(het_retina_vs_het_dlgn,
                   ko_retina_vs_ko_dlgn,
                   ko_retina_vs_ko_scn,
                   het_retina_vs_ko_retina,
                   het_dlgn_vs_ko_scn,
                   ko_dlgn_vs_ko_scn,
                   dlgn_kowt, dlgn_htwt, dlgn_koht,
                   scn_kowt,
                   retina_kowt, retina_htwt, retina_koht)

mm_tables <- combine_de_tables(mm_de, extra_annot=pair_mtrx,
                               excel=glue::glue("excel/{rundate}mm_tables.xlsx"))

## Writing a legend of columns.

## Printing a pca plot before/after surrogates/batch estimation.

## Working on table 1/3: retina_vs_dlgn

## Working on table 2/3: scn_vs_dlgn

## Working on table 3/3: scn_vs_retina

## Adding venn plots for retina_vs_dlgn.

## Limma expression coefficients for retina_vs_dlgn; R^2: 0.934; equation: y = 0.967x + 0.0347

## Warning: Removed 1 rows containing missing values (geom_vline).

## Warning: Removed 1 rows containing missing values (geom_hline).

## Warning: Removed 1 rows containing missing values (geom_vline).

## Warning: Removed 1 rows containing missing values (geom_hline).

## Deseq expression coefficients for retina_vs_dlgn; R^2: 0.822; equation: y = 0.955x + 0.0956

## Edger expression coefficients for retina_vs_dlgn; R^2: 0.917; equation: y = 0.977x + 0.0265

## Warning: Removed 1 rows containing missing values (geom_hline).

## Warning: Removed 1 rows containing missing values (geom_hline).

## Adding venn plots for scn_vs_dlgn.

## Limma expression coefficients for scn_vs_dlgn; R^2: 0.934; equation: y = 0.967x + 0.0347

## Warning: Removed 1 rows containing missing values (geom_vline).

## Warning: Removed 1 rows containing missing values (geom_hline).

## Warning: Removed 1 rows containing missing values (geom_vline).

## Warning: Removed 1 rows containing missing values (geom_hline).

## Deseq expression coefficients for scn_vs_dlgn; R^2: 0.822; equation: y = 0.955x + 0.0956

## Edger expression coefficients for scn_vs_dlgn; R^2: 0.917; equation: y = 0.977x + 0.0265

## Warning: Removed 1 rows containing missing values (geom_hline).

## Warning: Removed 1 rows containing missing values (geom_hline).

## Adding venn plots for scn_vs_retina.

## Limma expression coefficients for scn_vs_retina; R^2: 0.934; equation: y = 0.967x + 0.0347

## Warning: Removed 1 rows containing missing values (geom_vline).

## Warning: Removed 1 rows containing missing values (geom_hline).

## Warning: Removed 1 rows containing missing values (geom_vline).

## Warning: Removed 1 rows containing missing values (geom_hline).

## Deseq expression coefficients for scn_vs_retina; R^2: 0.822; equation: y = 0.955x + 0.0956

## Edger expression coefficients for scn_vs_retina; R^2: 0.917; equation: y = 0.977x + 0.0265

## Warning: Removed 1 rows containing missing values (geom_hline).

## Warning: Removed 1 rows containing missing values (geom_hline).

## Writing summary information, compare_plot is: TRUE.

## Performing save of excel/20200108mm_tables.xlsx.

pander::pander(sessionInfo())
message(paste0("This is hpgltools commit: ", get_git_commit()))
this_save <- paste0(gsub(pattern="\\.Rmd", replace="", x=rmd_file), "-v", ver, ".rda.xz")
message(paste0("Saving to ", this_save))
tmp <- sm(saveme(filename=this_save))